How to delete internal intesected faces?
Shrinkwrap is actually the best way I can found and it works pretty well. Comparing to the heightmap approach talked about here BlenderExchange, the shrinkwrap approach is easier to operate and involves less processes.

Here is how I do it, first create a plane mesh over the beveled object, subdivide the surface with 30 slices:

 

Add subdivision surface and shrinkwrap modifiers.  The subdivisions need to set to 4 or 5. The mode of the shrinkwrap need to be "Project" (You might need to turn on "Negative" if "Positive" doesn't work.)

 

Apply the modifiers and edit the mesh. To do this easily, go to a side view and box select the vertices on the top layer, remove the vertexes:

 

Then you get a beautiful top contour without internal intervening faces:

 

The shape will have more details then necessary. Use limited dissolve to fix that 



End result: